genome.fa.s8016.2.7.7.80.10.50.1000.16.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  5469637

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   

This is table  16  of  25  ( 2971 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3496216--3496341	46	2.8	45	89	3	191	30	22	7	40	1.80
3496276--3496344	19	3.1	23	64	28	58	28	21	10	39	1.86
3501664--3501704	22	1.9	22	90	5	66	36	7	12	43	1.70
3507858--3508015	21	7.8	20	73	7	95	39	25	16	18	1.91
3507982--3508211	20	11.5	20	86	1	246	37	25	17	19	1.94
3508889--3508935	24	2.0	24	87	8	69	25	14	21	38	1.92
3509108--3509132	12	2.1	12	100	0	50	72	0	28	0	0.86
3511466--3511597	20	7.4	19	78	18	158	14	22	17	45	1.84
3511447--3511597	53	2.9	53	97	1	286	13	23	17	44	1.85
3511447--3511597	33	4.4	32	71	21	126	13	23	17	44	1.85
3511656--3511766	52	2.1	53	98	1	215	45	18	23	13	1.84
3511707--3511798	33	2.8	33	98	0	175	45	18	21	14	1.84
3511726--3511780	14	3.6	14	73	21	56	45	20	23	10	1.82
3511811--3511910	19	5.5	19	84	12	147	15	23	17	45	1.85
3511794--3511910	53	2.2	53	95	1	209	14	24	17	43	1.86
3512017--3512053	14	2.6	14	91	0	65	45	21	0	32	1.52
3514031--3514087	14	3.7	14	77	20	60	45	22	21	10	1.82
3514012--3514104	33	2.8	33	93	0	159	48	21	19	10	1.79
3513975--3514109	19	7.6	19	75	16	119	46	23	18	11	1.81
3514105--3514214	19	6.3	18	71	20	83	9	17	28	45	1.78
3514105--3514196	33	2.8	33	93	3	150	7	18	28	45	1.76
3514258--3514731	93	5.1	93	99	0	921	45	18	12	22	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3516429--3516542	33	3.5	33	93	1	203	45	21	23	9	1.81
3516436--3516547	14	6.8	18	72	23	86	43	22	24	9	1.83
3516559--3516615	14	3.7	14	75	20	60	8	24	22	43	1.81
3516543--3516623	33	2.5	33	95	0	144	8	22	22	46	1.78
3516600--3516675	21	3.7	21	83	3	109	11	25	17	46	1.82
3516599--3516676	41	1.9	41	97	0	147	12	25	16	44	1.83
3516755--3516825	33	2.2	33	89	0	106	47	16	23	11	1.79
3517005--3517059	22	2.5	22	81	0	74	20	16	40	23	1.91
3517209--3517398	20	9.4	20	81	5	213	19	18	25	36	1.95
3517209--3517398	60	3.2	60	83	0	245	19	18	25	36	1.95
3517385--3517467	21	4.0	21	73	6	78	25	16	24	33	1.96
3517365--3517463	42	2.4	43	77	11	100	21	18	23	37	1.94
3531877--3532353	236	2.0	240	98	1	926	31	14	17	36	1.90
3537302--3537336	13	2.7	13	100	0	70	42	14	8	34	1.76
3539744--3539768	12	2.1	12	100	0	50	56	20	0	24	1.43
3540170--3540343	42	4.1	42	85	1	224	39	17	16	25	1.91
3541864--3541924	30	2.1	30	84	6	81	36	18	16	29	1.92
3541932--3542070	42	3.3	40	79	6	118	26	17	21	34	1.95
3544538--3544574	19	1.9	19	88	0	56	32	27	16	24	1.96
3544681--3544730	20	2.5	20	96	0	91	24	32	22	22	1.98
3545541--3545618	24	3.2	24	96	0	138	20	20	20	38	1.94
3546988--3547043	29	1.9	29	100	0	112	28	21	19	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3547875--3547917	18	2.4	18	92	0	68	55	23	4	16	1.59
3547975--3548257	140	2.0	140	97	0	530	28	13	14	43	1.83
3548228--3548304	20	3.8	20	94	0	127	31	20	19	28	1.97
3549948--3550049	21	4.9	21	74	4	89	24	20	34	20	1.97
3549928--3550049	42	2.9	42	79	7	140	23	18	36	21	1.95
3550518--3550559	19	2.2	20	91	4	68	47	23	14	14	1.80
3550580--3550618	19	2.0	20	90	5	62	51	20	15	12	1.76
3550619--3550667	20	2.5	19	83	6	62	14	22	16	46	1.82
3550676--3550724	20	2.5	20	89	0	71	20	20	24	34	1.96
3552639--3552775	20	7.2	20	73	9	90	41	21	18	18	1.90
3553150--3553206	22	2.6	22	88	0	87	19	19	42	19	1.90
3553371--3553441	20	3.5	20	74	11	81	22	16	28	32	1.96
3553357--3553461	41	2.6	41	93	0	183	21	14	25	38	1.92
3553357--3553461	21	5.1	21	71	13	92	21	14	25	38	1.92
3553487--3553523	19	1.9	19	88	0	56	24	16	27	32	1.96
3555005--3555067	25	2.5	25	94	0	108	60	0	0	39	0.97
3555353--3555410	30	2.0	30	83	10	75	41	8	20	29	1.82
3556541--3557066	43	12.0	43	73	12	250	26	18	5	49	1.70
3556542--3556732	42	4.5	42	77	12	149	24	14	6	54	1.62
3556568--3557067	87	5.7	85	74	13	352	26	18	5	49	1.70
3556555--3556791	129	1.8	129	81	8	295	24	15	8	52	1.69
3556728--3557067	139	2.5	139	82	8	382	26	20	5	46	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3556874--3557133	43	6.0	43	76	8	217	30	19	3	46	1.67
3556969--3557131	88	1.9	85	84	7	220	31	19	3	46	1.66
3559190--3559271	43	1.9	43	87	9	123	47	9	9	32	1.69
3559553--3559644	25	3.8	24	75	21	77	33	1	4	60	1.23
3561455--3561488	18	1.9	18	88	5	52	50	0	2	47	1.16
3561723--3561760	20	1.9	20	94	0	67	13	26	18	42	1.87
3561852--3561967	6	19.8	6	93	5	193	33	50	13	1	1.52
3562067--3562123	6	9.5	6	100	0	114	33	49	17	0	1.47
3561919--3562218	152	2.0	152	96	2	545	27	37	26	9	1.87
3567135--3567185	14	3.8	13	80	10	50	60	1	0	37	1.08
3577316--3577466	75	2.0	76	82	8	184	48	8	16	26	1.75
3586484--3586684	112	1.8	111	84	4	280	31	11	16	39	1.85
3587957--3588020	33	1.9	33	84	6	85	51	3	1	43	1.26
3588072--3588144	27	2.7	28	85	6	87	42	4	0	53	1.20
3588105--3588197	30	3.1	30	81	3	96	36	5	2	55	1.35
3588998--3589089	39	2.4	39	83	3	105	36	20	25	17	1.94
3589021--3589107	39	2.2	39	91	0	138	33	20	21	24	1.97
3589760--3589814	25	2.3	24	81	9	67	63	3	3	29	1.28
3590268--3590313	24	2.0	23	91	4	74	50	0	0	50	1.00
3590448--3590473	13	2.0	13	100	0	52	53	0	15	30	1.42
3593206--3593267	27	2.3	27	94	0	106	40	6	12	40	1.69
3595375--3596070	322	2.2	313	85	5	939	55	12	3	29	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3595422--3596067	102	6.2	101	71	17	351	54	12	3	29	1.52
3596792--3596898	42	2.5	42	96	3	196	27	3	27	42	1.72
3601009--3601083	38	2.0	38	91	0	123	32	10	13	44	1.78
3602974--3603043	31	2.3	30	82	4	86	45	7	2	44	1.46
3612467--3612502	15	2.4	15	100	0	72	41	11	16	30	1.83
3622836--3622895	30	2.0	30	96	0	111	30	5	20	45	1.72
3623076--3623142	21	3.2	20	83	12	82	17	32	14	34	1.91
3626368--3626427	30	2.0	30	96	0	111	30	5	20	45	1.72
3626509--3626587	21	3.8	21	98	0	149	20	35	18	25	1.95
3626650--3626696	21	2.3	21	96	3	87	19	34	19	27	1.96
3626657--3626709	12	4.7	12	80	20	69	18	37	16	26	1.93
3634719--3634767	18	2.7	18	93	0	89	26	34	22	16	1.95
3642652--3642694	22	2.0	22	95	0	77	53	9	0	37	1.33
3642654--3642702	22	2.2	22	85	3	62	57	10	0	32	1.32
3642657--3642972	80	3.9	80	84	6	454	52	13	0	33	1.43
3642704--3642782	22	3.4	22	74	16	79	53	15	0	31	1.42
3642754--3643151	32	14.4	31	68	28	253	52	12	0	34	1.42
3642737--3643026	54	5.3	54	82	14	387	52	13	0	34	1.43
3642786--3642828	22	2.0	22	95	0	77	51	11	0	37	1.39
3642813--3642869	18	3.4	18	67	18	59	54	14	0	31	1.40
3642788--3642836	22	2.2	22	85	3	62	55	12	0	32	1.37
3642652--3643151	134	3.7	134	87	6	476	52	13	0	34	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3642674--3643027	166	2.1	166	97	0	663	52	13	0	33	1.43
3642876--3642949	22	3.2	22	73	19	62	52	17	1	28	1.53
3642952--3642994	22	2.0	22	100	0	86	51	13	0	34	1.42
3642954--3643002	22	2.2	22	88	3	71	55	14	0	30	1.40
3642754--3643106	80	4.3	83	83	9	415	52	13	0	34	1.43
3643037--3643151	54	2.1	54	96	0	212	52	11	0	36	1.38
3643086--3643186	22	4.5	22	71	7	94	50	9	0	39	1.36
3643131--3643233	15	6.5	15	78	15	100	49	2	0	47	1.16
3643076--3643233	69	2.3	67	86	6	212	50	6	0	43	1.27
3643214--3643268	26	2.0	27	89	6	85	49	7	1	41	1.41

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25